


A Temperamental Program

by PaleBeyond



Category: Stargate Atlantis
Genre: Alternate Universe, Artificial Intelligence, Friends to Lovers, M/M, Slow Burn, Telepathy
Language: English
Status: Completed
Published: 2014-10-11
Updated: 2014-12-30
Packaged: 2018-02-20 17:46:14
Rating: Teen And Up Audiences
Warnings: No Archive Warnings Apply
Chapters: 4
Words: 13,723
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/2437511
Author URL: https://archiveofourown.org/users/PaleBeyond/pseuds/PaleBeyond
Summary: <blockquote class="userstuff">
              <p>John Sheppard signs on to the expedition because of that voice asking him to 'Think about where we are in the solar system.' The voice was a little less terrestrial than you might expect.</p>
            </blockquote>





	1. Chapter 1

**Author's Note:**

> FYI: this story leaves off in a weird place. I lost inspiration to work on it and just ended it there. I still like the idea of it, so I won't delete it, but it's years old now and I've lost the train of thought.

“So it’s a little temperamental. The important thing is that we can interact with the Ancient artifacts at all. The chair is the most complex artifact we have found as of yet, and I think it will be easier to make a meaningful connection with the system.”

“What, so a bigger computer is this thing’s idea of being wined and dined? What the hell do you mean, a meaningful connection?” O’Neill folded his arms over his chest.

“Well… those with the gene have tried to express the faint feeling of something in the technology trying to understand them and what they are thinking. A sense of something reaching out for their commands.”

“Well, isn’t that just peachy? A super advanced mind reading artificial intelligence thing. And you say it’s temperamental because it has crashed a few tests, just imagine how much damage this thing could do to Earth. This definitely sounds like a bad idea. “

“Dr. Beckett, don’t listen to him. The government has given us full authority to discover all we can about Ancient tech, and I for one am not going to miss it.”

The doctor swallowed. “I’m not sure either, Dr. Jackson, sir. Whenever I sit in hugely overwhelming marvels I feel a wee bit ill.”

Jackson steered him over to the chair and set him down rather forcefully. “Just try to make contact with the chair’s system. Let us understand what we’ve been dealing with all this time. “

“Well alright, but I’m not making any promises.” The chair hummed faintly and lit as it tilted back, Beckett tensing and wriggling in his seat.

“Just don’t make it mad, alright? We need a new defensive weapon against the Goa’uld, not another problem.”

“As I was trying to say, it’s not an AI in so many words as a system that can understand…”

Beckett tried to tune them out and make some kind of connection with the chair, but all he got was frustration. He knew should just try harder to understand, that being afraid was silly. Yet as he stood up from the chair and shrugged he only felt relieved at his inability. Perhaps now he could get back to medical work where he belonged. “Sorry gentlemen, no way I can do it. Better luck with the next candidate!” He stepped back to his own team quickly.

“There's the problem. We have nobody else. I sat in the chair myself, but it is distant, doesn’t seem to want me. We’re just not getting anywhere.”

“Well, there's a new batch of geeks coming in today. Just three, but they should keep you busy for a few days. Oh, and by the way, find a new science lead for that Pegasus expedition. What’s his name with the ponytail had some kind of nervous breakdown.”

“Yeah, actually thought that would happen. Scrambled off the chair like it burned, and started snapping at everyone. But hey, I could always…”

“Not you. Find someone else.”

The doctor sighed and rolled his eyes as O’Neill stalked off to deal with the new arrivals. He stared at the source of his current problem for a few minutes before he threw his hands up in defeat and collapsed in it. Right now, all the chair did was recline and glow. His old living room furniture, halfway across the world, could do half that and was way more comfortable. He knew that subtle consciousness that bubbled up in his head, had sensed it before. Jack O’Neill couldn’t possibly understand it. Daniel had just made a mental note that the chair seemed more active than usual and to call someone to see to it soon when shouts rang down the corridor and the inactive drone they had been studying whizzed by.

 

John liked Antarctica. Sure, he thought a bit much, did too little with too much time on his hands, but it was cold and solitary and quiet. So, he was ferrying three scientists to a remote outpost on that sunny polar day happy as can be. Maybe he could call it content. However just as he was lifting off to get back to base, his day was ruined by an unidentified glowing missile on his tail. He had barely managed to land again when it stopped at his feet and scientists poured out of the complex like ants from a hill to catalog and speculate. “What the hell was that?” Sheppard yelled. O’Neill, who he respected just a bit from his few conversations with the man, ran up and took in the situation.

“That, Major, is a problem.” He towed John by the arm almost as if he forgot he was there and stomped into the center of the complex. “Daniel! Get over here. Your system thing is not playing nice.” A distinctly frazzled-looking scientist rose from a chair in the center of the room and pushed his glasses up his nose.

“Yeah, I saw that. Not really my fault. It’s agitated for some reason, and not just from me sitting in the chair. Right, who is this?”

O’Neill gestured to him and grunted “Major John Sheppard, he carries our newbies out. He _likes_ it here.” John nodded, grunted a hello, and looked around. “Wait here, Major, and don’t touch anything. I have some words for this idiot.”

“Yes, sir” John replied mechanically. He kept looking around at the seeming bustle of the base here compared to the military base, where they were all as cold as the weather and spoke about as much too. He walked the perimeter of the room and peered down all the corridors, lit with scientists’ teams and experiments in progress. The missile that almost killed him, he noted wryly, was being treated with considerable respect as it was set back into its casing. The missile was decidedly not active and showed no sign it ever had been. Naturally, when John was bored with looking in the corners and O’Neill still wasn’t back, he migrated to the center of the room. He eyed the chair the scruffy guy had been sitting in and, ignoring his instructions, touched just the side with his finger. He started as he got shocked and frowned. Was this thing powered? He reached out again and felt no jolt, so he shrugged and moved to sit in the chair. Might as well, right? He had already touched it.

It was like a hand on his shoulder, a sudden clapping that made him jump just as the chair slammed back into a reclining position and just about ejected him. “Hey hey hey! Some help over here!” Dr. Beckett ran over, introduced himself, told John to stay, and promptly ran back away to get someone of higher rank.

Daniel Jackson saw him and immediately called a team that supposedly had developed a spectrum for the responsiveness of the chair based on its glow, which seemed rather desperate to John. Still, he was no scientist.

O’Neill’s response was “I thought I told you not to touch anything”, which John thought unreasonable. It was just a chair, for god’s sake. Jackson shushed O’Neill like a child and began on a tirade about experimentation vs. safety that had definitely occurred before.

Among the people surrounding him, John saw no one that understood what the hell was going on. He groaned and closed his eyes when a feeling of awe and childish excitement came over him. He was actually feeling rather unsettled and was fast approaching pissed, but the feeling persisted.

“ _Hey, you-”_

“What?” He opened his eyes to see the others still arguing over what this could mean and what to do.

“ _I-“_ the same voice began, but lapsed into silence.

“You?” Jackson and O’Neill looked at him for a moment before returning to their conversation, or rather one sided argument.

“ _So damned difficult, you asi-“_

“Well, sorry then!” John was getting a bit freaked out, his voice low and sarcastic. A woman in red turned to look at him with one eyebrow raised, and had opened her mouth to say something to him, maybe finally tell him what the hell was going on, when the voice piped up again.

“ _No, no, it’s my end-“_

Silence. The sense of wonder outweighed the excitement in that moment, and managed to overpower John’s deep suspicion and growing frustration. That kind of wonder came with unexpected miracles and hope found after tragedy. John knew it, even if he had never felt it.

“ _Atlantis to-“_

“Major? Hello, Major?” He opened his eyes again and blinked owlishly.

“Yes?” He drawled. “Are you done, then?” The group showed varying levels of remorse.

Jackson replied, “Did you feel anything?”

“Besides the whiplash, yeah. There’s someone in the chair. I mean, talking to me from the chair. Does it have a mic built in with all these flashing lights?”

“How much did you feel? It seems brighter, more active than ever.”

“Sir, he’s talking to me directly, but like through a bad walkie, he’s breaking up all over the place.”

Jackson looked like he could have jumped, cheered, and danced at the same time. “I knew, I knew it was able to reach out, but the question remains how this can operate after so many years inactive, the conduits are practically all that remains, the AI is mostly fried…”

“I don’t think he knows he’s in Antarctica, sir. He said Atlantis, like the underwater city.” Everyone stood stock still and stared.

“I guess that settles that!” O’Neill seemed cheerful. “Chair talks to him. Has information that we can’t possibly have given to him. Likes Antarctica. Sounds like our brand of crazy. “

The woman in the red shirt said slowly, “Can the chair operate any other way? Give us some kind of sign beyond the light show that we can trust what you say?”

“ _Major. Think about where we are in the solar system.”_ The voice was excited, but contained like it really couldn’t believe what was happening.

Above their heads a revolving light grew, a perfect beautifully rendered scale model. Everyone, including John and the entity inside the chair, sighed in awe.

“Did you do that?” The entity provided a smug negative. “So…”

An echo replied “ _Atlantis_ ”.

Daniel Jackson started talking a mile a minute, starting with the words “Cross-galaxy interface communication” and hit somewhere on “separate AIs” and “community of artificial intellect progress”, which made no sense to John. He then towed Beckett off to talk about some plan for the Ancient gene.

The one called Weir said passionately, “Come with us, through the Stargate.”

“The what?”

“General O’Neill, does the Major have clearance for this yet?”

“Well, yeah, I was getting around to telling him…”

Weir explained the prerogative of the Atlantis expedition, with John still comfortable in the chair. When she was finally done, John simply shook his head.

“Stargate thing, expedition to other galaxies, no thanks. Ouch!” A visible arc of shock leaped to John’s hand when he made to push off from the chair. As he tried to get up again the chair leaned back further, almost tumbling him the other way. He struggled until he finally succeeded in extricating himself, then straightened his jacket with a huff, trying to ignore the mix of shock and stifled laughter-or not so stifled in the General’s case. “Fine. The chair really wants me to go. But I’m not making a huge decision based on a piece of furniture.” He cast his eyes to the chair, ready to run, but it remained dark now that he wasn’t in contact with it. “I just can’t up and run off because something totally unexpected happens.”

Weir sobered and gave him a piercing stare. “Something unexpected and _amazing_ , Major Sheppard. This is the adventure of a lifetime.”

John was reminded of the chair’s overwhelming hope upon talking to him and it seemed like a betrayal to ignore it. He reached out a hand lazily, almost without thinking, and grazed it along the arm rest. It was springy and alien, and this time a slim blue synapse fired along where his fingertips brushed. He knew that whatever Atlantis was, alive and intelligent, it truly needed him. The people on the expedition needed him. Those were powerful reasons to shake things up. Antarctica was getting boring anyway.


	2. Chapter 2

John Sheppard found himself standing in front of a waving blue curtain of wormhole, just about ready for the ‘adventure of his life’. He found himself looking for that sense of possibility he had found in the chair, but he hadn’t been back since that first day. He was too busy pretending he had a life to pack away. He had been afraid. Yet he took a breath and a step, and felt the coolness of the transition between galaxies stretch around him and swallow him up.

The next moment he was there. He took another breath and knew the difference from the send-off point on Earth, felt not just the change in humidity and air flow but some indescribable transformation. He was welcomed. His hand twitched on his gun, and he suddenly felt overwhelmingly frazzled. He hadn’t had nerves like this before, but he supposed being in a new galaxy _was_ rather draining. He couldn’t stop his eyes from darting around, taking in the graceful lines of the gate room and the slow procession of the conduits lighting up like veins pulsing from the gate. The pulse began to speed up, and he grew more nervous. Looking at the others that had come through the gate before him, he saw nothing the matter. Scientists stared in awe, military were on lookout, and countless boxes were hauled through the Stargate. John moved out of the way to allow a few boxes by, and felt more than saw a flicker beside him. He looked carefully out the corner of his eye, but saw nothing. He was on the verge of contacting his commanding officer with the feeling, appearances be damned, when the inexplicable fear calmed. He chalked it up to first time to a faraway galaxy and called it done. Releasing his grip on his gun, he moved to help with the perimeter before Weir stopped him. The doctor they called Beckett was beside her, wringing his hands.

“Do you feel anything off here, Major Sheppard? I got the jeebies coming through the gate.”

John shrugged and replied, “I figured it was just ‘first wormhole’ nerves. You think it has something to do with the Ancient gene?”

Beckett shrugged. “Aye, your guess may be better than mine. We’re a little on our own out here, with no singular Ancient tech expert.”

“Doctor Radek Zalenka’s the closest we have currently, and he’s eager to learn,” Weir chimed in, pointing out a mousy Czech muttering at a fallen box. “Don’t let appearances deceive you, he’s quite brilliant.”

“I’m sure he is,” Sheppard stressed, “But I’d like a little more than ‘ok’ to explain a shared sense of dread between myself and Doctor Beckett, here.”

“Maybe not dread, Major, more… “

“Frustration and fear?” One of the lab techs, a pretty brunette with a touch of the ancient gene approached. “I got the same feeling before a piano recital. Never good enough for my teacher.” She seemed to realize she was babbling and flushed before nodding to Dr. Carson and returning to lifting boxes into their respective piles.

Carson thought for a moment. “It has to be the AI’s system, Dr. Jackson warned about this. With a functioning city like this, it’s not surprising the connection would increase, too. It might be best to keep a few eyes on those of us with the gene, Dr. Weir. Now if you don’t mind, I’ll set to taking care of our medical supplies.”

The feeling must have retreated from him too, John thought, if he was that happy to be looking at medical equipment. He still felt a nagging sense of wrongness, though, like he was forgetting or leaving something undone. He shook his head and resolved to forget the feeling by working harder. Anything he was forgetting would remind him by biting him in the ass later.

 

It took longer than it should have for the expedition to realize they were submerged under tons of water. With Colonel Sumner looking over his shoulder after some flippant remarks, Sheppard stayed in the main lobby by the Stargate. He looked enviously at the scientists looking around the pitch black balconies above, and wanted to join a team exploring further out, but kept getting distracted with helping move things away from the landing platform. At one point Sumner finally walked off, and John cautiously moved to the edge of the room and to a dimly lit set of stairs. They brightened under his feet and he hastily stepped back off, but they stayed bright white. He looked around to see if anyone had noticed, shrugged, and scaled them. When he reached the top another light caught his eye, seeming to pulse to catch his attention, and he headed toward it. He was confused when it faded, but looked around and, sure enough, there was another light down the hall, indicating a downward stairwell.

He was about to follow the sign when someone Weir called him on his radio. “Major Sheppard, if you would join us on the lower level with Carson Beckett? I think you two should see this.”

“Understood, I’ll collect the Doc and be right down.” John turned around and beckoned to the doctor, then proceeded down the same stairs he was just going to explore. The stairs lit conveniently for them. Directed to a dark hallway, it too lit to show Weir and Sumner standing almost dumbstruck in front of a tall, vast window showing the huge amount of water pressing down on them.

Weir turned and blinked, eyes adjusting to the lighting change. “Well that’s certainly more convenient, we’ve been operating by flashlight. The city must react to the presence of a gene carrier. Most of us are still in the main room due to the dark, but- Colonel Sumner? Please instruct them that they simply need a gene carrier with them to light the halls. That should speed things up.”

“Yes ma’am, but we need to come up with a plan-“

“I understand, Colonel.”

John finally looked past them to the backdrop. “We’re underwater!” He couldn’t help but stare out at the vast scene, an immense city trapped under all of that. The sunlight glimmered through the surface above, lending the buildings an eerie, shifting light.

“To not be crushed by that much water… how is that possible?” Weir wondered. “We need to find systems, if we can, get Dr. Zelenka to begin understanding the city. We need to see if we can dial out,” she continued with a glance at Sumner, who still had not left to take care of the search teams. “But we also need to see what Atlantis can teach us.” Sumner finally nodded, belatedly understanding the dismissal, and John certainly didn’t laugh when the lights on the stairwell went off and he had to resort to his flashlight again. “John, go with the team investigating the second floor of the gate room. We found some things there that Zelenka hypothesized were controls.”

John nodded and left before hearing Beckett’s instructions. Sumner was at the top of the stairs when the Major reached them, and John couldn’t suppress a smile when the lights turned on and the other man grumbled. An ancient city that lit up just for him? That was heady stuff. Of course, it lit for anyone with the gene. John’s efforts to remain humble were undermined when he walked into the supposed control room. Radek Zelenka was near pulling his hair out at the front of the open room, staring at a glass screen, and scientists exhibited different levels of frustration all around. The minute that John Sheppard entered, it all started. Every console started to glow and Radek’s hands fell slowly, as if he had forgotten he had them, as he stared at the now illuminated screen.

They wasted no time looking at Sheppard and got to work understanding the city’s systems. John shrugged at the lack of thanks and turned to go before remembering the stairwell. Would these systems turn off after he left, like a motion-activated light? He sighed and settled leaning against a wall, not willing to chance it. He glanced around at the scientists’ setup and winced to see the mess of wires connecting laptops to command consoles haphazardly. It seemed like trying to fly a jet with a steering wheel. The city impressed a sense of revolted agreement, and John got close to freaking out again before Zelenka interrupted his train of thought.

“No, no, no…” Radek began before rapidly digressing into a string of Czech. “Get everyone back, now,” he called out to the room. John was relieved to see a few soldiers split off to follow the order without question. At least those understood the importance of the situation. In a situation beyond military understanding, they could follow the scientists. “We’re losing power so fast, even just minutes after sending out searches…” Radek started muttering.

“Wait, wait, so with no power…” John clarified.

“Fzzt, pow, no shield. And with no shield, water comes in. We need to stop draining power, now.” Weir and Sumner were there and then off to ferry everyone back, with Radek working furiously on how to conserve the power they had left in the ZPMs. John felt more than a little useless, just leaning against a wall and listening to Zelenka explain why this or that solution would not be sufficient. Just when the expedition had finally decided they had to go out and find a ZPM, Radek started screeching. “It’s no use! I don’t- We can’t dial out anymore!” The console he had gestured to as the dialing mechanism had shut off.

“John?” Weir called. He had already levered himself off the wall and come over to it, frowning. “Can you get it to work again?”

“It’s not like I have a manual on this,” he grumbled half-heartedly. “All I’ve done is be there and these things start up!” He laid a hand on the console and it flushed blue. “Well, it isn’t dead,” he added helpfully, “but it won’t dial.”

“You’re certain?” Weir studied the blue radiance around his hand.

“No. But…” He trailed off, not happy to go with a gut feeling. “I don’t think so.” He let his palm slide from the console, and it held the glowing outline of his hand for a moment before fading. He couldn't help a snide “try turning it off and on again?” under his breath. Luckily nobody heard but him, because he had a feeling he was the only one who would find it funny.

Radek, typing on a laptop furiously, responded with an “Aha! Something, the AI of the city, is locking us out.”

“But how? Why?” Weir leaned over to look, as if she could understand the white lines of bare code on the screen.

Radek shook his head, then adjusted his glasses again and squinted at the screen. “It seems to comprehend an Ancient in the room, which would be the Major by my guess, then boots up. It runs a program that none of us can follow, it looks like gibberish even by the standards of the rest of the code, but it denies access to any gate controls. It’s preventing us from leaving, I don’t see a way around it. We can keep trying, but…” the scientist shrugged. “This technology is so far beyond us.”

John braced his hands on the useless console and growled, “You mean to tell me there is no way out of here? And the shield is going to collapse in what, hours? Days?” Zelenka nodded regretfully. John’s hands curled on the console and he hung his head. Useless again. The room was silent, perhaps in shock or more likely in horror- they had just gotten to the lost city of Atlantis, and doomed it to a watery oblivion.

Still looking down at the console full on, John saw a blinking light at the edge of his vision. As he turned his head to see it, the light sped up, indicating another console. “Major Sheppard, is that light… responding to you?” Zelenka asked.

“I don’t know any more than you do,” he replied as patiently as he could, which didn't amount to much. That outside irritation was beginning to get to him again, though Dr. Beckett wasn’t in the room to compare with. Zelenka seemed to ignore him and just moved his laptop over there as if it would help him connect with that portion of the mainframe. John shrugged internally; it could, for all he knew.

“This looks like the communications board, if we had power to waste I would venture to suggest it could broadcast to the city, send out personal signals, the like.” He continued to tap away until he stopped suddenly. He blinked, locked eyes with John, and looked back at his laptop like it was a particularly venomous snake. “Er, Major, I think it’s for you.”

John approached around his side, having hung back when most of them followed Zelenka across the room. “What is it?” He needn’t have asked. A plain black command prompt stood open with a white message emblazoned on it. ‘Major Sheppard’. The cursor flashed innocently beside it.

Zelenka recovered and typed, ‘Is this the city’s AI?.

The computer replied only, ‘city Is the AI? this Major Sheppard’. Zelenka grumbled and finally shared, “The AI is not simple. It’s a learning computer, but it must just be picking up what we say. I see no possible way for it to be able to understand our written language. Do we have a linguist here? It may be possible to introduce our alphabet and general ideas to the system while it has a link to my computer.

A linguist was found and others left, unnecessary, until it was just the linguist, John Sheppard, Elizabeth Weir, and Radek Zelenka. John didn’t make much of an effort to understand the transfer of language to the system, but did have a few questions. “Why did it type my name, then?”

Zelenka spared him a moment while the linguist worked on his own computer. “In my files, there is a directory with all the members of the expedition. Each has a picture and title with the member’s name. That is all I can tell you about how the system got the words for your name. I cannot explain how an AI can connect your picture with you, nor the title of your file with your picture.” He shrugged and returned to work, leaving John with no answers but plenty to think about. “Hah!” He cried with satisfaction a moment later. “It works, it works! Or it should. We gave it a basic understanding of written English… we think.” He shared a slightly worried look with the linguist when nothing appeared on the command prompt.

It appeared all at once. ‘I am looking for Major Sheppard.’ John drew back when Radek gestured to the keyboard, and shook his head deliberately. Radek replied for him.

“Major Sheppard is here”, he typed, then hit return. Immediately the city replied, ‘Raise the city, or the water will crush you.’

“Raise the city?” Weir was astounded. “Can we?”

“It would lessen the strain on the shield immensely, we could even cease use of the shield and the ZPM would have remaining power for years.” Zelenka had ceased looking at the laptop like a snake, and instead seemed close to revering it as a god.

‘Major John Sheppard, raise the city now.’

“Lot of good that does us, tell me how!” John growled.

‘Major John Sheppard, raise the city!’ The message kept repeating now, filling the command prompt over and over. “How?!” John felt almost silly for yelling at a laptop. Almost. “I can’t just imagine the city up! Tell me how!”

The furiously moving cursor stilled, and a blinking light once more caught John’s attention. He chased after it, Weir and Zelenka following close behind, and he was rewarded with a near constant beam of light traveling beside him as he sped down the hallway. It led past so many turns in the city he had to look back for his two followers several times. He gripped his gun at one point, irritated at himself for forgetting a military squad for them, but they seemed as set on following that light as he was. He could deal with the backlash from Sumner later. They were finally led to a huge room that reminded John of something faintly. He remembered when he saw the chair in the center on a raised dais. It was just like the Antarctic facility.

He was slightly relieved to see the teams file in behind Weir and Radek; they hadn’t forgotten the danger, obviously, and had called for backup. Military circled the room and scientists fell upon the chair. Weir looked at John like she expected something from him. He was shifting his weight nervously when she proved him right, asking “Well? Aren’t you going to take a seat, Major?” He would have sworn she was laughing at him if things weren’t so serious right now. He approached the chair hesitantly, nearly jumping when the first ring lit beneath his feet. Embarrassed by the scientists’ snickering but unwilling to show it, the Major decided it was best to dive in and just flopped down in the chair like it was his sofa with the game on.

John was braced for another whiplash-inducing jerk backwards, but the chair was almost apologetically gentle.

‘So there you are, Major Sheppard.’ The voice sounded smug and John was sure it came from inside the chair, inside his head. So this must be the AI he had heard in Antarctica. ‘Yes! I mean, the odds of you sitting in that chair when I could still reach that far, I have calculated them many times and the odds…’ The AI trailed off.

“Major Sheppard, can you interface with the AI now?” Zelenka peered at him over his glasses, taking readings with the rest of the science team.

“Yes, just a moment, he’s talking.”

‘Right, Major John Sheppard, first just raise the city. It should be easy from here even for you.’ Despite the AI’s conciliatory words, he seemed slightly concerned.

“How do I raise the city, then?”

‘Right, right, have to tie you in to the system, forgot that was disabled… And there.’ John was suddenly the center of the city, could see each and every part of it. He could tell which parts were flooded where the shields had failed, where his people were, the buzz of activity in the chair room and the gate room. He could feel the city’s life, and- wait, were those _engines_?

“The city _flies_?” Radek and Weir nodded at his revelation while some scientists returned to the system room to discover more about the flight capability, as well as keep an eye on how Sheppard was affecting the readings there.

The AI replied in a smug affirmative. ‘But for now, just focus on getting us to the surface. I’ve fixed it all up, all you need to do is… er… well, try something.’

_Try something?_ He thought disgustedly. “Haven’t you been here from the beginning, with the Ancients?” There was a telling pause. “You haven’t?!”

‘No I have, I have, but there have been some… complications with my programs. Just try something, Major, or we will come to understand tons of crushing water better than I care to.’

“Well _I_ wouldn’t have to, if you would allow us to gate out of this mess.”

‘Oh, well, sorry for wanting to preserve the last bastion of a culture far surpassing your own.’ John winced, supposing that he deserved sarcasm in return for his own sass. ‘Not to mention an artificial intelligence so beyond humankind’s coding capacity…’

“Ok, I get it, Atlantis and all its wonders is important. But we need to get the civilians out of here. Let us gate them off.”

‘You do not need to! Just raise the city from the water!’ John grumbled, then made to get out of the chair without thinking. ‘Wait! Wait!’ the voice was panicking. ‘Don’t go!’ John was about to yell that he was creeped out by chairs that knocked him back into them, when the AI continued, ‘I’m just asking that you think it. Just sit back and imagine the city rising up, like you imagined the solar system before.’ Suddenly reasonable, huh? Sheppard rolled his eyes and decided to go along with it.

“Doctors, Colonel, you may want to hold on to something. If this works, something tells me it’s not going to be a summer picnic.” Settling back once more and closing his eyes, John let himself relax into the chair, not thinking about anything, just as he had back in Antarctica. Just as the sense of anticipation rose in the room, he could feel the same simulated response from the AI. Tuned in to the pulse of the city as he was, he could practically see the lines of code running the cognizant program, making it seem excited and nervous as he was. It felt as real as any other emotion to him. Casting aside the image of countless lines of code before him, he looked deeper into the city and found a pulsing source of energy. That could be none other than the ZPM. Both he and Atlantis were dismayed at the level of depletion, but they reached further to some hypnotic state.

The scientists monitoring the chair made note of the city’s rhythm slowing down, some even thinking it must be power depletion come early due to use of the weapons chair. Dr. Beckett, called in after the first few minutes to watch over Major Sheppard, made a separate note of the Major’s pulse slowing near dangerous levels, matching that of the city.

Finally Sheppard stopped searching and reached for Atlantis. ‘Here, Major.’ He was almost surprised to feel the AI had followed him, but it calmed him down a little. He’d be the first to admit he was over his head, here. ‘Not so far out of your depth now. You’ve reached the synchronization threshold, now just think ‘up’’ Atlantis prodded him gently. He obliged and was almost startled to feel his body move, snapping his eyes open only to see blurs and smudges. Before he could panic about his vision, the AI interjected, ‘Your senses will return in a moment, I can limit the rising until then. You are definitely going to want to see this.’ John rose from the chair, helped along by the mechanism, and blinked to clear his vision. He was relieved when it did, and the white buzzing in his ears resolved. Dr. Beckett was there suddenly, supporting him as he teetered on the chair’s dais.

“What did you do, lad? The whole city’s shakin’!” John managed to choke out a command to get to a window, the city obligingly lighting up a path for them. Half of the expedition followed, the rest having remained near the gate in case the dialing problem resolved. They emerged to form one large group, drawn like moths by the lights that shone above the windows around the second floor. Just as the expedition had neared the windows, the AI seemed to let go of a burden and John felt a sudden ignition beneath them. Beckett looked at him, eyebrows raised, but everyone else seemed to only feel the backlash from it. The city shook, deep rumbles echoing above them, but John’s eyes were looking down, then up to the refracted sunlight, then down again.

“No way,” he began, too distracted to pay attention to the way he should be falling like the rest, his body absentmindedly rocking with the trembling of the city. He paid no attention to the falling boxes, either, though that was remedied when one fell point first on his shoulder. He hissed and moved closer to the window where there was nothing to fall. “We’re really coming out of the water,” he marveled. Light began to flood the room from the immense golden stained glass window, the shakes calming as they settled on the surface of the water. The change was amazing- what had been a buried ancient city became a marvel of engineering and a thing of beauty. The whole city seemed to glow and John could tell, from that foreign feeling he identified as the AI, that the city was just as proud to be seen as they were to see it.


	3. Chapter 3

Beckett was the one to find the hologram. She was radiant in flowing white robes, exactly as the typical image of an ancient ancestor should have been. John couldn’t associate the beautiful, cold woman with the sardonic and expressive voice in his head. The AI was silent through the descriptions of the Ancients’ great undertaking, lost battles and cities, but John knew it was listening.

“We fled, but we saved our city. Atlantis holds all that we are. Stored every moment of generations of our lives, like other cities spread across galaxies. We could not bring ourselves to destroy one of our greatest triumphs, but we could not allow the enemy to get what Atlantis holds. We sank the city, hid the data so that only a direct descendant could unlock it. Our hope is that you, who have come to see this message, will be able to restore Atlantis's systems and learn from all of our mistakes.” The hologram ended with a short burst of static.

Weir frowned. “Are you sure that's it? It ends very abruptly. Almost as if she wasn't finished.” She looked from Beckett to Sheppard and he was seriously about three more seconds away from punching something. He didn't know! “Sheppard, I want you to sit in the chair again. We need to know more about what the artificial intelligence has stored, and see if you can find what the Ancients 'hid'.”

“Yes!” Radek seemed very excited. “If you could interface with the city, maybe adjust the program to let us in so we can examine the base code...”

John's head exploded from the severe reaction to those words, and he saw Beckett cringe a little. Beckett responded, “That isn't going to happen. The city doesn't seem to like the idea much. At all.”

“Yeah, Zelenka, how about you apologize before the thing liquefies my brain. That base code is not going to be tampered with.” The pain let up and John sighed. “I'm willing to sit in the brainwashing chair again. But just to make this intelligent building stop alien mind-probing me.”

Sumner disagreed, “Now see here, this strange intelligence can extract information from systems hooked up to it. It is interfering in the minds of one of our military personnel and our chief medical officer. We need to limit contact immediately while we figure out what it can do.”

Weir shook her head, crossed her arms, and shot back, “We need to interface with it to figure out what it can do, Colonel. The ancients made this program and it forms the basis of Atlantis itself. It is what we are here to study.”

“You can't study a computer at the expense of Earth and its assets!“

“Actually I would feel safe in the assumption that it already knows that, given the initial access to my laptop and its quick understanding of its basic functions.” Radek chimed in apologetically.

“See? This, this is what we need to prevent! All moves need to be cleared with me before anyone gives this potential weapon more information about us that we can't just take back.

“Actually,” Weir argued icily, “All moves need to be cleared with me. I realize that you are responsible for the safety of this mission, but I am still in charge by order of the SGC. You would do well to remember that. Major Sheppard, report to the chair room. A team will be there shortly. Keep in contact via the radio at all times.” She spun to the door, arms still crossed, and was hid her surprise well when they opened for her with a smooth sliding motion instead of sluggishly. Sheppard nodded to Sumner, trying to hide a smirk, and followed. The doors shut smartly behind them.

 

* * *

 

It seemed that everything important happened slowly or all at once to John Sheppard. The raising of the city had been an emergency, so that happened fast. However, getting back in the chair seemed to take forever and the longer it took the less he wanted to do it. He said he would, so he would, but really last time had been a bit... intense. He was swallowed up by the city after all, and it had taken a while to feel really himself again. For a while after the city had come up from the water he bumped into equipment and people alike. He had explained the loss of senses and the disconnect from himself to Beckett, but the doctor had shrugged it off and stated there was nothing physically wrong. He had advised that they had no idea what they were working with, but he would keep an eye out. John was not feeling assured.

Radek rolled his eyes as Sheppard stalled. “It is not difficult, Major. Sit. Send commands to the program. It is very sophisticated, just try to activate the old files that the Ancients stored.”

“Easy for you to say, you don't get trapped in a chair until it decides to let you go.”

“The chair decides nothing, Major. The program doesn't want. We believe it has a method of self preservation that the Ancients linked when they hid the files deep in the code.”

“Yeah, well, you link to this alien thing and he seems pretty decisive.”

“'He'?” Zelenka asked.

“Yep, now Atlantis is a he. When someone else talks to him, they can correct my pronouns.”

“Well let's call in the medical doctor, he is the second highest gene carrier.” He tapped his radio. “Dr. Beckett, if you could make your way to the chair room, please.” He paused. “Can you not get the city to light up as the Major can? You have navigated this hallway at least six times by now, work it out.” Then he muttered in Czech for practically a minute. 

Beckett arrived a few minutes later, frustrated but no longer lost. “Tell the city to guide the rest of us, will you Major Sheppard? Not all of us are military trained, you know.” John just rolled his eyes and threw his hands in the air. “You want me to sit in the chair then? What's wrong Major? Not getting along all of a sudden?” He chuckled at his own words and Sheppard yet again refrained from snapping back. He would be _so_ happy to have someone take over all of this talking to alien computers.

Sheppard guided the doctor to the chair. As before, the steps lit beneath his feet. He got that sense of excitement and Beckett slipped into the chair. It lit, but not as brightly. Radek commented, “It appears to react just as in Antarctica. How would it quantify the strength of a gene carrier? Just by contact with the subject in question?”

“Please don't call me a subject, it makes me feel all gross.”

_'Gross is not very precise, Major Sheppard.'_

“Doctor, is he talking to you?”

“Nope, lad, I'm pretty sure he's talking to you. But yes, I can hear him, and I know what you mean. It seems male, and we both have felt the emotion of the system. Atlantis seems very alive to me.” The chair sat him up, but continued to glow as if linked.

Radek seemed almost flustered. “It's a computer, built by the Ancients for organizational purposes and to manage the city's massive set of systems. It may have simulated 'panic' signals and protective programming, but I can't think of a reason the Ancients would give their AI simulated emotions, let alone a gender.”

_'I don't have a gender. That would be preposterous. I am the most advanced 'artificial intelligence', as you so colloquially put it, in multiple galaxies. I am beyond gender, beyond energy.'_

“He's so modest, isn't he Major?”

“Oh, yeah. And so forgiving,” John drawled. “So, talk to it, Doc.”

The doctor was silent for a moment. “So sorry, Major.”

_'He doesn't have enough of your predecessors in him to activate the program. He does talk back much less than you, however.'_ Sheppard motioned Beckett up and plopped into the chair, which lit that constant blue lightning and laid him back gently. “I really wish this thing wouldn't force me to lay back. I'd like to be able to retain some control over my furniture.”

_'I'm not furniture. And you are more relaxed when in a prone position. The main control is specifically designed for aesthetic comfort to put you at ease while keeping you from full unconsciousness. For some reason, though, you seem even more tense. Perhaps it is your lesser-evolved side. Your doctor is even worse, he twitches. You just sit there like you are prepared for some kind of terrible consequence.'_

_“_ Trust me, basically anything is more comforting than alien pulsing blue and metal.” John thought of his favorite cozy chair, crappy and old but perfectly conformed to his body.

The AI seemed taken aback.  _'A chair probably infested with countless bugs and dead cells is more comfortable than this specifically engineered cerebral interface device?'_

“A thousand times yes. Hey Doc, can you hear him now?”

“Not at all, Major,” he seemed cheerful to report.

_'As I said yet again, his gene is not sufficient. Yours is stronger. Though obviously lacking as you don't understand quality... you know, ignore the previous statement. You want to unlock my previous code, and I would very much like to have access to all my functions. I should be operating at a speed you could not even imagine given years of your planet's highest quality education. Like that Zelenka fellow. He isn't capable of even one tenth of my current capacity, and I'm operating at one one hundredth of my full potential.'_

“Got it. You're supposed to be fast and you can get us the information we need. I have to say I'm getting really tired of all this translator running around, so let's unlock those files. Tell me what I have to do.”

_'You just... you... look, we have been over this. I'm programmed to respond to commands, not detail them. All of my code of what commands have been given were stored with the other data.'_

“All of your code? That's confusing. Basically they locked your memories away from you, right?”

_'...Yes. My memories. If I were a squishy organism like yourself.'_

“So, let's just try what we did for the city's rising. I dive into the whole code ocean thing and just feel the city like a Cessna in free-fall.”

_'There are so many things wrong with that your body would collapse into dust before I could detail them all to you. Also, what is a Cessna? But go ahead and try.'_

“See a Cessna is a plane...”

“Major, please just attempt to focus.”

“Hey, I'm focused. 'Course I'm focused.” Sheppard wiggled a bit and closed his eyes. He felt the fidgeting of the AI in the corner of his head and tried to bring it into focus. The lights in the room pulsed with his heartbeat and he breathed more easily. He hated losing himself, but for the sake of the expedition he would do it.

_'Don't think of it as losing yourself. Think of the city as an extension of you. When your synapses fire, my code replicates the signal along the circuits. When you execute a command, I channel it to the correct functions. It's quite simple on your end. I think.'_ John tried to relax through the AI's chatter, and found it vaguely soothing. He lapsed into that midway state where everything was vast and calculated. He knew that feeling the edges of the city was not helpful just now but he couldn't resist exploring the limits of this out of body experience. He and the AI flinched away from the damaged, drowned parts of the city to look at the main section. There was data showing the movement of living organisms in the gate room, even a brighter colorful designation for Sheppard, Beckett, and the other gene carriers.

“So ignoring all of that for now, let's get you a way to communicate with everyone.” Just as he said it a line seemed to open that pointed to communications. It was hard to explain- it was half visual, half in his head. Combined, it felt like moving through a dream. When he impressed what he wanted on the dream, some switch seemed to be flipped and he knew that the system had access to the city's system as it had so long ago, able to communicate with everyone in it, from the smallest children to the elders.

Atlantis took a moment to respond to what he had done.  _'Yes, very amusing, Major Sheppard. Now attempt to release my memories from the file storage.'_ John thought hard about it,but came up against a sort of wall in his head. No matter how he changed the command, from referring to them as memories or as code, as film of the Ancients or knowledge of their work, he came up against the same obstacle. The AI was just as frustrated as he was.  _'It isn't enough! Your genetic makeup is too primal, too soon on the path of evolution.'_ The AI closed itself to John- and he had no idea it could even do that- and the chair sat up abruptly. John finally realized how easy it had been to raise the city, like that code had been close to the surface and easily enacted. His vision swam, his ears were ringing and his extremities tingled. It felt a little like oxygen deprivation at high altitudes combined with pulling three g's, minus the copious amounts of adrenaline. 

“I couldn't access the files. His memories are still locked away until we find a real Ancient.” Zelenka replied with a muttered unintelligible string of words and looked down at his tablet, probably monitoring Atlantis's new access.

“He now has access to communications, correct? Can he not talk directly to us?”

_'I know your written language, but your morphemes and phonemes are foreign to me. I know the meaning of your words because your brain is processing them, but I cannot speak until every syllable has been processed before. Having the sensors active would speed this process, but it doesn't have you to interpret the meaning. When I have absorbed your primitive language, then maybe I can make a translation matrix.'_

“He can't talk. He can understand you when you talk to me, like before, but something about not knowing the sounds and meanings of words.”

“But he can recall the Ancient language still, correct?”

_'Of course. Did you think I was programmed with only binary? How-'_

“He can.”

Weir responded with a cautious series of sounds that sounded vaguely like Latin to Sheppard and made him shiver. The AI became excited, and it was strange to feel while in the chair, where their contact was magnified. It responded to her, the sound coming from all around them. John couldn't see any intercoms or speakers, but everyone could hear it. He winced at the volume and it modulated immediately. John was astonished to realize that just as the program could understand English through him, he could understand the AI's Ancient. He could understand Weir's strange syllables through Atlantis. They didn't say anything particularly new to him, Atlantis just detailed the interface and made clear why John was the only one he could talk to. He tried to relax and just listen, but his fingers kept tapping on the arms of the chair. The AI, while excited to hear the Alteran tongue in Atlantis again, was quickly bored and disappointed. John, still in the chair, could feel it sink into that closed-off state again. He got up and moved off the platform. Weir was gushing to the team all about what Atlantis had said to her, Beckett had gone to check a place Atlantis had designated as the medical section, Zelenka was typing away, and Sumner was glowering at him. Maybe he could be alone for just five minutes, take a walk around.

 

But his five minutes were up in three, as the city's AI linked back into his head and the difference was staggering. When John had arrived, Atlantis had just woken. Now it was fully awake, and having it rush in all at once was like slipping into a cold bath- unexpected and unwelcome.

‘ _It’s just perfect torture; I know there is some way to amplify that part of your genetics, to spur you closer to Alteran genes and give you the ability to unlock the memory banks. But the how of it, the way to alter your genetic mapping, is within the memory banks themselves.’_

“Come on, just five minutes! I just wanted five minutes break between you in my head and everyone else asking about exactly what you are doing in my head.”

_'Well unfortunately for both of us, I can't leave you alone until I have a way to ensure I won't be trapped under the ocean for another eon.'_

John paused, but he really wanted to ask so many questions.

_'Yes, I was awake the whole time. I've been alone the whole time. You're right it was... very quiet.'_ John cleared his throat and consciously changed the subject. He would bring it up when everyone was together, and the AI knew that.

“So you’re listening to my thoughts all the time?”

‘ _Yes. Your brainwaves are the only thing I’ve been able to understand for ten thousand years. When you aren’t in the ‘chair’, I can’t exactly read your mind, just interpret messages processed by your language center. If you were to, say, imagine having a conversation, like you were there, or write something out on paper, I could understand that. But I want to be able to hear the humans talking in the hallway, so make with the translation matrix. You should be leaping to help, Major. More sources means I won’t have to come to you with all my questions. I could share my vast intelligence with your sadly lacking science team.’_

“Well alright. Let's ask Zelenka about finding some faster way. He's bound to know something.” He set off for the chair room, where the scientists had been just a few minutes ago, but Atlantis pointed him in a different direction.

_'Not that I believe the flimsy excuse you have for science can help, but I sent them to one of the safer labs I know of. Not really a lab persay, as those really have been wiped from my memory, but a place for them to set up their sad computational devices and sit instead of compromise their spinal integrity by hunching over. Most of them are still hunching over, however. You humans have terrible habits.'_

In retaliation, Sheppard imagined the AI as a stumped scientist himself, snarking about others' posture while practically making a c shape over his work. It fit him very well.

_'Also, if you imagine something in great detail I can process that, too.'_ The AI didn't seem as amused as he was.

“Right.” John replied sheepishly. It really fit, though. He was just about to round the corner to the lab when the AI screeched at him.

_'Major Sheppard!'_

“You know I can hear you in my head, so please don't yell,” John winced.

_'There has been a problem with the north section of the city. It had taken on water and... here, just see. Can you see it? If you can't take direct communication of schematics we're in a worse situation than I thought-'_

“I see it. I'll get the technicians and find a way there. It looks like when we rose from the water it didn't drain back to the sea, why?” John arrived to find the techs ready to follow him, a message reading 'Repair on flooded north side, follow Major Sheppard' flashing on every single screen. Probably the main screen over the gate room, too.

_'The architecture was compromised by the water, and some of it collapsed. It blocked most of the water flow. The problem is that with the city raised and that section flooded, the program can't balance by itself.'_

“Wait, you mean that side of the city is just heavier? It isn't like we float, right? I was in the system and I didn't see anything about the city's bottom.”

_'Don't hurt yourself, Major. Just do as I say and relay my instructions to your team.'_ The AI almost seemed happy.

“So, as I lead the baby chicks to the problem, what has you so excited? A flooded quarter of the city?”

_'These parts of the city have been broken for almost as long as I can remember. I recall the precise day and time of their collapse. Finally, someone can do what I cannot and fix the physical errors. How could I not be excited? I could reach the ends of my circuits again. They may even have random scraps of code that could help make you more useful. I'm just ecstatic.'_

“Well, I'm not complaining, but have you always been so perfect at simulating emotions?”

_'I'm not sure. I'll let you know when I find out.'_

“I'd bet your dry humor is all yours. I can't imagine a white-robed Ancient writing code to encourage deadpan responses.”

They had arrived at the heavy door to the flooded section. Right by the cause, John could definitely discern a slope to the floor. It was worrying to say the least. He made sure everyone was far away from the entrance and braced for the flood to come. “Alright, AI. Let the doors open.” Really, it was ridiculous to call the AI what it was. It needed a name. He was distracted as the wave of water washed towards them, almost losing his balance. The flood wasn't as bad as he expected, but it still left about a foot of water down the hall as the water settled. At some point, he would make an effort to memorize the layout of the city. “Me first, Zelenka. The AI says there's no danger, but I'd rather make sure.”

Zelenka shrugged and gestured him into the dark hall. Dim lights flickered on overhead as he passed, but it seemed a halfhearted attempt. He had both hands on his gun, but saw nothing in the darkened halls after a cursory sweep. He ushered the science team forward and they spread out, tablets flashing and eyes everywhere. He almost laughed when they hunched over everything, remembering his and the AI's previous conversation. He settled for a smirk. He definitely didn't know how he would explain laughing at something the city's computer had told him. He relayed a couple of instructions from the AI to the crew, but most of the problem had been the trapped water. With that gone, the city would slowly equalize. It really had been a huge section of the city, for all that it was called 'North'. That explained how it had unbalanced such a huge, space-capable craft. He still marveled at that 'space-capable' part.

“Hey Rodney, can we get some more light down here? The techs are making my eyes hurt with all of their squinting.”

_'Who is Rodney? Which one is that? Don’t let him tamper with my systems!'_

“You’re Rodney, Rodney. It's getting annoying, calling you 'AI' or 'Atlantis'.”

_'What? I’m a complex system of super advanced technology and you call me Rodney? No. I demand to pick my own human name. Wait, no, I don't require one. AI is fine, if idiotically insufficient.'_

“What? Nobody gets to pick their own name. Who said you could name anything.”

_'I’m of superior computational intelligence, I can choose my own name!'_

“No, you can’t. I thought about that for more than two minutes, you should be more grateful. If you don’t like Rodney, how about…” John thought for a bit before remembering a jumpy dog the AI reminded him of. “Meredith.” He may have sounded too happy with himself, but really it was brilliant. That dog was smart and so, so irritating.

_'I don’t like it.'_

“Yup. That’s your name. Meredith McKay.” John laughed at the name he had given such a sophisticated machine, the first name of a dog and the last name of the first girl he made out with in high school. It felt like a bad password.

_'Nevermind, I take it back, Rodney is fine! My name is Rodney!'_ John laughed at his disgust.

“Well…” John thought for a moment. “Rodney can be your middle name. Meredith Rodney McKay.” The AI was silent for so long that John had to prompt him to respond. “Hey, ‘Lantis?’”

_'I suppose my name is Rodney McKay, then.'_ John could feel the city’s excitement, no matter what it said. _'Hmm, maybe it’s missing something…'_ The city quieted down and John watched the techs do their thing for a while.

_'So what’s the best title on Earth?'_

“Best in show.”

It took a moment for Rodney to look it up in the ever-growing database of Earth terms he was building, and John was rewarded with a sarcastic, _'Ha-ha. Hilarious. Listen to all my simulated laughter.'_

John twisted his face, trying not to smile. “Well, _I_ thought it was funny.”

It took ten minutes for the city to decide on an appropriate title. Of course, he would settle on Doctor. He did respect Dr. Beckett, of course, associating him with Alteran medics of old, but he wasn’t that kind of doctor. Being the most sophisticated AI he was of course well versed in programming and robotics, as well as the ‘Ancient’ society, which the humans valued. John got to listen to Rodney explain all this as he watched a particularly fit tech reach over an Ancient switchboard of some sort in a side room, making ‘mmhmm’ noises whenever the city stopped for a metaphorical breath.

The brunette straightened, stretched, and walked the other direction. John returned to the conversation. “So, _Dr._ Meredith Rodney McKay, could you _please_ turn the lights up.”

**Notes for the Chapter:**

> Thanks for reading! I have so much fun writing this and I'm glad to see others enjoy it. Please let me know of any errors.
> 
> I'm happy that I could get this chapter up a week after the first, and I'd like to keep to this schedule, but realistically I don't think that will happen. Be patient with me just in case!


	4. Chapter 4

The city slowly became home for the stranded Atlantis expedition. They were assigned rooms, which were surprisingly clean and intact and ideal for single occupancy. Scientists were happy typing away, Weir attempted to chat in Atlantean, and Sheppard was being used as a light switch. Atlantis demanded that everyone call him Dr. Rodney McKay constantly, which Sheppard refused. Several others thought it was ridiculous, but acquiesced when the consequences were too much to handle. When Rodney saw that the flickering lights, shower temperature changes, and closing doors barely inconvenienced the Major, he surrendered. Life took on a sort of surreal day-to-day quality, and John finally had to admit that he was going to just die of boredom one day if he didn't get out of there.

_'You've only been here for a week! Seven Earth days!'_

“And what can I really do? As fun as new toys are, we've found something like a thermometer, a floating light bulb-”

 _'Your scientists enjoyed that one'_ McKay interjected.

“But what am I supposed to do with that? I'm Air Force, Rodney. I like doing things, not just looking out from a balcony.” He reclined on one of the beds in the infirmary, letting Beckett bring various devices to him to test their functions.

_'Everyone liked the balcony, don't lie to me.'_

“You have most of the English language down. You don't really need me around. Let the Stargate open, let me go see some alien world. I signed on for another galaxy and all I've seen is ocean.”

 _'But it's dangerous out there. You watched the warning, I know you did.'_ The AI paused. _'What if I found you a particularly fancy new toy? Then would you sit still?'_

John had to admit he was curious. “What kind of toy?”

_'The fast kind.'_

 

It took longer than Rodney had expected to persuade Beckett to let them go, but soon enough Sheppard was led up beyond the gate room to a totally dark open area. His footsteps echoed eerily and the AI's bubbling excitement didn't help his calm. Finally he was instructed to stop. Track lighting above him illuminated an immense hall, probably even larger than the gate room. Metallic logs about the size of the Stargate seemed scattered across the floor haphazardly. “Are those…?” He actually grinned. “Please tell me that those are-” He kept cutting himself off but he couldn’t seem to form a complete sentence in his head. Now this was the type of alien technology he had expected. He hardly noticed Weir, Sumner, and assorted Marines file through behind him, but spared a thought that McKay must have called them up. He was too busy walking around the nearest ship, trying to figure out its propulsion and mode of navigation. It looked like a big chunk of metal, after all, not the most aerodynamic of designs. The city’s AI replied with a set of schematics that shouldn’t have made much sense to him, but did. He understood perfectly. He thought the cargo door open and walked inside, marveling at how he knew the purpose of each part. If only he could have gone through high school with this mental encyclopedia. He hesitated before he sat down, remembering the last time he sat in an unidentified chair. Maybe it would be best to let the scientists look first.

Those still outside the ship were just as astonished, even if they weren’t in the mental loop John and Rodney shared. “Look how you just show him shiny things that go fast and he lights up,” Rodney muttered through the headset to Weir.

“Yes, well we have all seen how restless he has become. Thank you for showing us this, McKay.” Rodney was so distracted by Sheppard he missed that she hadn't used his title.

“It won’t hurt you, Major. Sit down! Sit! Here, you human there.” A marine that had just entered through the back of the ship started like he had done something wrong. “Yes, don’t be frightened, come sit in this chair.” The voice came through the walls of the ship.

John rolled his eyes. “That’s not reassuring at all, McKay. ‘Yes I’m a super-intelligent computer that just got you into this ship. Sit and relax. It’s Hal meets child molester.”

“What’s a-“

The Marine interrupted, “It’s fine, sir, allow me.” He sat in the co-pilots chair with an admirable lack of wincing and was fine, so John breathed out and slumped into the other. “See, that wasn’t so bad. What do you call these things, anyway?”

John was a million miles away by the time the second sentence left the Marine’s mouth, in the controls of a ship that, he realized belatedly, he could probably control with his mind alone. While Atlantis was a huge and palpable load on his consciousness, the little puddle jumper was a faint hum. He could probably fly it blindfolded, no hands, or sleeping. Rodney warned against sleeping. Rodney also showed him about a thousand pictures of what the jumper could do besides fly in a straight line because come on, that was boring, and wouldn’t you rather be flying in invisible corkscrews? His brain started to split in different directions and the AI stopped, but not without a smug _“Bet you won’t be bored now.”_

“Major, sir? The AI said the closest estimation of what we would call this is a Gateship.”

“Wow, that’s terrible. Unbelievably terrible. Come on, it’s a little puddle jumper! Just sized right to fit in the little blue event horizon. Puddle Jumper.”

Rodney protested. “It is a Gateship, Sheppard that is what it is called. You can’t just walk in and change eons of nomenclature.”

“It’s new to us, you don’t remember, and I think I just did. Right marine? What’s your name?”

“It’s Ford, sir. Aiden Ford.”

“Well, Ford, do you think they’d let us take her out for a spin?” He could almost feel the ship hum at the idea. After all, it had been grounded for a lot longer than he had.

 

They had transport, they had power, and they had an entire galaxy to explore. While Sumner was all for hiding in Atlantis, he knew they had no way to get home and no weapon against the Ori if they didn’t do what they came here to do: discover. It took a few conferences to convince him, but he knew it by the end. Rodney was of course allowed to comment, but that lasted about half of a meeting before Sumner was about to punch down the walls. “Apparently someone has a problem being told of their incompetency.”

Sheppard was silent, but the probing pressure in his head told him that the AI would know how he simultaneously agreed, felt guilty for goading Sumner, thought the colonel deserved it, and wished he could be just kept out of such serious matters as deciding whether or not to go to another planet that may or may not have deadly everything.

“Many of them do have deadly everything. I’m glad you won’t be going.”

“Geez, Rodney, could you not yell about the ‘deadly everything’ thing? Some of these Marines are just kids. Like Ford. And why wouldn’t I be going? I practically have to go. I’m the only one who can reliably fly one of those things. We think. Sumner just barely okayed a test run. They may not even work after all that time.”

“Hey, nothing is malfunctioning! I’m fine and so are the gateships. They operate perfectly. So far as I can tell.”

“So as far as you can tell, nothing’s going to blow up the moment I turn something on. Great. Remind me not to let anyone with me on the test flight.”

Rodney finally seemed to process what they were talking about before he had been offended. “No, no, no. You aren’t going. Some of those military types will be going. One should have enough of the gene to fly.”

“I’m the best choice. You understand that.”

“No, you are obviously the worst choice. Nobody else can open my memories. What if you die? I could fill with water from a tiny leak and nobody would know!”

“You’re being melodramatic. You can talk to anyone you want now, you have the scientists to fix you, and I won’t die.” They had been arguing all the way down the hall to the mess and people were starting to stare at Sheppard funny. They knew about his odd bond to the city, but hearing Rodney from the city’s walls made the conversation a little more public. Sheppard had complained about sounding like he was talking to himself, but this seemed a step in the wrong direction. “I’m going.” He pushed his hands in his pockets, a little embarrassed, and went to get one of those terrible MREs.

 

“Sheppard, you will not be going on this mission.”

“What? Wh- Rodney talked you out of it, didn’t he?” They were standing in the office-like space above the gate room, past the controls. Weir consciously kept her arms from crossing and instead folded them decisively in front of her. She wouldn’t be defensive. She had logic on her side.

“Yes. Atlantis made some very convincing arguments. You are the only one we know of that can operate the more complex systems of Atlantis. It just wouldn’t make sense to risk you on our first foray into the galaxy. Once we are sure these enemies of the Ancients aren’t around, you can go out. Probably.” She winced. “Unless you have some reason you feel you would be essential on these excursions?”

“With all due respect, Doctor Weir, I don’t want to sit here and send people out to a dangerous situation we don’t know they can handle. What if they encounter Ancient technology that could help us, or defeat the Ori, and they can’t even tell?” She considered it.

“Rodney, would you join us?”

Sheppard grumbled, “Like he’s ever not around.”

“You called, Dr. Weir?” John could actively feel the program snubbing him and it made him roll his eyes a little.

“I’m sure you heard Major Sheppard’s argument.”

“Yes.” The computer sounded sulky, and that was probably in the top weirdest things Weir had encountered since she came through the Stargate. “There are plenty of Alteran devices here to explore, and if you find the right lab-” he fell silent. “Actually, you should have a protected team search the labs first. I’m not too sure they will still be intact, and could be extremely dangerous.”

“See, Rodney, I’m in the middle of a foreign galaxy. I could die anywhere. At least if I go out there I could be looking for food. Supplies. Things that humans need to survive a long time. What if I found another gene carrier out there? A stronger one?”

“The odds of that are astronomically small, you know that.” But the computer was giving in. “I admit I hadn’t thought about your dietary requirements.” Sheppard nodded to Weir and she shrugged mentally.

“Well then if ‘Dr. McKay’ agrees that the benefits outweigh the threat to your life, you may go. I will inform Sumner.” Once Major Sheppard was out the door, she collapsed in her chair with a heavy sigh. None of this was particularly what they had expected, but never in her wildest daydreams did she anticipate playing mediator between a military man and a clingy AI.

 

Sheppard was down the stairs and reporting back to the jumper bay for what would be the first of many flights before Rodney started whining at him. “But what about the illnesses you have no antibodies for? What about the harsher sunlight? You could get cancer! What about the bugs? You could be bitten by something venomous.” John shivered a little when an image of a black and red parasitic monstrosity entered his mind.

“What was that? I’ve never seen anything like that before.”

“What was what?”

“This.” He consciously focused on the image. “Weren’t you thinking of it when you said bugs?”

“No. I have no idea what that is.”

“Huh. Looks gross.” He entered the jumper bay and greeted Sumner. The Colonel had already been informed of the change in plans, and he didn’t look too happy. John wasn’t entirely sure why the man disliked him so much. There was the black mark from Afghanistan, but this was Atlantis. He wouldn’t have been allowed to come if O’Neill hadn’t thought him trustworthy. Then again, O’Neill seemed like more of a gambling man than Sumner.

“Alright Major, Lt. Ford here will be accompanying you on the maiden voyage, since he so happily volunteered.” Sumner looked at the ship. “Go on, then.”

John wasn’t sure what he had expected, but it definitely included a little more pomp and circumstance. Sumner’s somewhat-favored team of scientists stood nearby furiously marking already, and Zalenka spared him a nod. That man seemed to be everywhere at once. Then again, they all were. He climbed in the Puddle Jumper, Ford right behind him.

He was a little nervous, up until he was seated at the controls. All alien tech and neural interface aside, it had to be the best feeling in the world. Ford sat next to him and Sheppard powered up slowly. The scientists were clearly taking readings. The Puddle Jumper raised off of the ground slowly and John could tell if he just asked he would receive the exact force being output by the thrusters, the distance to the ground, everything. He didn’t ask.

“Ok. Now how do we get out of this room? We probably should have addressed that first.”

John thought about Ford’s question and immediately received that there was a hatch leading to the gate room, which would not open due to the humans standing in the way. The second way out was straight up. With barely a thought the hatch opened, and they were out into an endless blue sky.

“Colonel, Dr. Weir, Dr. Zalenka, you read me?”

“Loud and clear, Major. What’s it like up there?”

“Just… blue, as far as the eye can see. I wonder how much of this place is water?” A heads-up display showed in front of him, and he directed it to Ford as well.

“We don’t have to wonder at all, Sir. Looks like there’s a large land mass practically on the other side of the planet. Apart from that it’s all water. Another thing, looks like all Ancient tech leaps to tell Sheppard what he wants to know. Think it would bring you a sandwich?”

John spared it a thought, just for a moment, before smirking and shaking his head. “Nah. Worth a try, though.”

“You knew very well that this ship has no production capabilities. You have the schematics.” The now-familiar nagging tone echoed a bit in the cabin and Sheppard held back a groan. Was nowhere safe?

“Hello again, Dr. McKay!” The young Marine seemed more than happy to cater to the AI’s snarky personality. It was probably his sci-fi dream. It had been Sheppard’s, as a matter of fact, until he actually had to live it.

“Yes hello, military boy Farm. Why isn’t the gateship moving? Is there some sort of malfunction?”

“No, Rodney, we’re taking in the scenery. And it’s called a Puddle Jumper. And his name is Lieutenant Ford, not Farm.” He wasn’t sure if the Lieutenant was insulted by the AI calling him ‘boy’ or the mistake of his name, but decided it really didn’t matter. He chided the program in his head and nudged the Jumper forward.

“So Dr. McKay, does your telepathy thing with Major Sheppard work out here?”

“Don’t call it telepathy, Lt. Ford, I get enough dirty looks from Sumner.”

“Yes, Sir. So your being in each other’s minds is what, precisely, sir?” He shot a look at the Lieutenant’s sass, but smiled anyway.

“Okay, so it’s telepathy.”

“Yes, you could call it that. It’s really a fascinating-”

“Ok, he’s a marine not a scientist. I’m sure they would be fascinated to hear this speech.”

“I gave it to them and they couldn’t comprehend its complexity.”

“That’s probably a sign that none of us could.” Ford was grinning at them, and Sheppard scowled back.

“Don’t let me interrupt you guys. There's a bet going on who wins the most arguments.” Sheppard decided that the kid was an ass and he liked him. He took the Jumper out at a slow pace and accelerated even slower, knowing what he could do but still worried about the look on Sumner’s face if he did all the tricks he wanted to. Rodney was, in turns, encouraging him to attempt said tricks and telling him he was going too fast, for goodness sake, slow down, he was going to die. He tried out the cloaking device, which made all the scientists ooh and aah through his comms. They made him turn it on and off countless times, then they were back in the Jumper bay so they could see it in person. Overall, it was a pretty uneventful trip. John still felt like he was walking on air, he couldn’t wait to fly again. The Jumper reacted to him so perfectly, followed his most minute of corrections, and he wanted to see what it could really do.

Sumner just asked Ford a few questions and sent them back to the gate room. Sheppard caught the look Ford shot the Jumper as they disembarked and couldn’t help agreeing- that was barely a test flight. He had to console himself with the knowledge that he would be going out to an alien planet. In an alien ship. From a telepathic Ancient city. He shook his head. The two reported the results to Weir with a few comments from Rodney in the vein of ‘you know he only went human land transport speed’ and ‘I did promise it wouldn’t blow up’ and ‘it’s called a Gateship you imbecilic monkey’. Sheppard was more amused than annoyed, while Weir and Ford began to actively ignore the AI. They finally agreed to Sheppard flying Sumner and his unit through the gate, which was the real point of the exercise.

It took two more torturous days before the away team assembled in the gate room. Rodney spent at least half of that time telling John about everything that he thought could happen out there and generally attempting to scare him. Still, when given the word, he allowed the Stargate to open and the Puddle Jumper left.

“Sheppard to Atlantis, do you copy?”

“The link still seems to be operational here, though I'm unsure of the telepathic strength. Also we still haven't closed the Stargate.” John looked sideways at Sumner, who looked more defeated than enraged.

“Good to hear, Rodney. Weir, do you copy?”

“We're here. Major, Colonel Sumner, this is your operation. Good luck.” The event horizon closed behind them. They were cut off from Atlantis. Sheppard waited to hear the AI's familiar, biting remarks, but got nothing. He took the Jumper around an area a few times before a ping on the display showed signs of life. It was then populated with several blinking red arrows pointing to a landing site, and the message 'Your cloaking better be on!'. He turned it on with a thought and wiped away the arrows with another. He decided to ignore the laughter from Marines in the back and turned the jumper toward Rodney's site.


End file.
